I pretty much design everything using Cadtools...
Cadtools will calculate square footage on any shape you select, if shapes are stacked on top of each other or masked, it will add all the shapes together that are selected or masked.
When you mask something, since it will combine the background shape(s) with the mask shape... I always select the mask shape using the "DIRECT SELECT tool to determine the square footage.
Remember, it will only count the square footage of the actual shape, so it's an odd shape - like you mentioned, it will only calculate that shape... if you need the overall square footage, I draw a box around it and CadTracker will calculate that box (if thats the only shape you selected)
If you have shape on top of shape (say 2 stars - but maybe one is offset a little, and select both, it will calculate both including the overlapped area... when I need an overall square footage of the 2 stars only, I will copy all the shapes, Pathfinder>Unite - then you will get the overall square footage of both shapes "welded" together.
Geez, it's really easy but when I explain it, it seems hard.